Just had this and replacing the spark plug wires took care of it. Mine was a slow progression. slowly got worse over 2-3 years. sometimes it was OK and other days it was bad. Dealer looked at it 3 times and did not find a good fix. I was check all those things you checked ( still need to replace the O2 sensor) and found that the wires were old and the spark had to jump a gap in two of the wires.
So New wires, new cap and rotor while your at it. clean and regap all the plugs, or a new set and see how she runs.

For you info you do not need a angled spark plug connector on the 560SL on the right side bank as all the web sites say. the angled connector is required for the W107 that still has the battery in the engine compartment.

Dave

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1970 220D, owned 1980-1990
1980 240D, owned 1990-1992
1982 300TD, owned 1992-1993
1986 300SDL, owned 1993-2004
1999 E300, owned 1999-2003
1982 300TD, 213,880mi, owned since Nov 18, 1991- Aug 4, 2010 SOLD
1988 560SL, 100,000mi, owned since 1995
1965 Mustang Fastback Mileage Unknown(My sons)
1983 240D, 176,000mi (My daughers) owned since 2004
2007 Honda Accord EX-L I4 auto, the new daily driver
1985 300D 264,000mi Son's new daily driver.(sold)
2008 Hyundai Tiberon. Daughters new car